vtools-filter docs

README.md

+vtools
+======
+
+Little toolset operating over VCF files. Uses cyvcf2 and cython under
+the hood for speed.
+
+
+Tools
+-----
+
+### vtools-filter
+
+Filter VCF files based on a few criteria. Will output both a filtered VCF
+file, and a VCF file containing all the filtered-out variants.
+
+####  Filter criteria
+
+| name | meaning | optional |
+| ---- | ------- | -------- |
+| NON_CANONICAL | Non-canonical chromosome | Yes |
+| INDEX_UNCALLED | Index uncalled or homozygous reference | Yes |
+| TOO_HIGH_GONL_AF | Too high GonL allele frequency | Yes |
+| TOO_HIGH_GNOMAD_AF | Too high GnomAD allele frequency | Yes |
+| LOW_GQ | Too low GQ on index sample | Yes |
+| DELETED_ALLELE | The only ALT allele is a deleted allele | No |
+
+#### Configuration 
+
+Configuration of filters goes by a little JSON file. See [here]() for an 
+example, and [here]() for the json schema.
+
+
+#### Usage
+
+```bash
+Usage: vtools-filter [OPTIONS]
+
+Options:
+  -i, --input PATH                Path to input VCF file  [required]
+  -o, --output PATH               Path to output (filtered) VCF file
+                                  [required]
+  -t, --trash PATH                Path to trash VCF file  [required]
+  -p, --params-file PATH          Path to filter params json  [required]
+  --index-sample TEXT             Name of index sample  [required]
+  --immediate-return / --no-immediate-return
+                                  Immediately write filters to file upon
+                                  hitting one filter criterium. Default = True
+  --help                          Show this message and exit.
+
+```
+